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<i>Bacillus subtilis</i> was applied in peat-based soilless cultivation systems containing a mixed substrate (peat:vermiculite:perlite = 2:1:1, <i>v</i>/<i>v</i>/<i>v</i>) and irrigated by one-strength or four-strength Hoagland’s nutrient solution to explore whether it can alleviate inhibition by higher-nutrient solutions (four-strength) and bring benefits to improvements of quality. The results showed that higher-nutrient solutions improved the flavor quality of cucumber fruit; especially, the contents of (E,Z)-2,6-nonadienal and (E)-2-Nonenal were effectively increased, which are the special flavor substances of cucumber. <i>B. subtilis</i> K424 effectively improved growth performance, photosynthetic capacity, vitamin C content, soluble sugars, soluble protein, and total pectin in cucumber under higher nutrition solution conditions. Compared with the higher solution treatment, the bacterial diversity significantly increased, whereas the presence of fungi had no significant difference following the <i>B. subtilis</i> K424 application. Moreover, <i>B. subtilis</i> K424 reduced the relative abundance of <i>Actinomadura</i> and promoted that of the <i>Rhodanobacter</i>, <i>Bacillus</i>, <i>Pseudomonas</i>, <i>Devosiaceae</i>, and <i>Blastobotrys</i> genera. Redundancy analysis showed that <i>Bacillus</i>, <i>Rhodanobacter</i>, and <i>Blastobotrys</i> were positively correlated with the substrate enzyme of sucrase, catalase, and urease. This study provides insight that <i>B. subtilis</i> K424 mitigated the deleterious effects of high levels of nutrition solution on cucumber growth and quality by improving the substrate enzyme, regulating the microbial community structure, and enhancing the photosynthetic capacity.